Let's unlock UNLOCK
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Presentation given during the opening of UNLOCK, an open infrastructure for exploring new horizons for research on microbial communities. Its four complementary research platforms are discussed: Biodiscovery, Parallel Cultivation, Modular Bioreactor and FAIR Data platform. Additionally, practical information for potential users is presented. This presentation was given on November 3rd, 2022 at Wageningen University & Research.
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Let's unlock UNLOCK
- 3. …TO MICROBIAL COMMUNITIES Folded Paper
- 4. MANY PARTS ARE THERE ALREADY
- 5. • Begrijpen en gebruiken • Evolutie is niet echt iets wat we nog begrijpen • Samenstelling / samenwerking evolutie… • Biotech is groot maar is gebaseerd op maar een eeh klein deel van de treasure chest • Current biotech based on low hanging fruits • Second generation biotech should be based on thorough understanding of the whole orchard • All current knowledge is based on cultivation of single microbes • < 1% of diversity • In complete afwezigheid van complexity / synergy TIME FOR SOLUTIONS INTEGRATION PARALLELISATION STANDARDISATION
- 6. INTEGRATION OF COMPLEMENTARY PLATFORMS
- 7. PAST PIONEERS IN FUNDAMENTAL AND APPLIED MICROBIOLOGY 1670 1890 Antonie van Leeuwenhoek Martinus Beijerinck
- 8. PRESENT PIONEERS IN FUNDAMENTAL AND APPLIED MICROBIOLOGY
- 10. AN OPEN INFRASTRUCTURE FOR EXPLORING NEW HORIZONS FOR RESEARCH ON MICROBIAL COMMUNITIES Unlocking UNLOCK 03 November 2022 Haans Design
- 11. Hauke Smidt Laboratory of Microbiology Wageningen University & Research Robbert Kleerebezem Department of Biotechnology Delft University of Technology Peter Schaap Systems & Synthetic Biology Wageningen University & Research Alette Langenhoff Environmental Technology Wageningen University & Research Photo by Sven Menschel MEET THE PLATFORMS
- 13. Automated sample processing platform Isolation and high-throughput cultivation of micro- organisms and consortia Single cell platform Geared towards strictly anaerobic micro-organisms BIODISCOVERY PLATFORM
- 15. SAMPLE PROCESSING UNIT Highly automated, high throughput Extraction of relevant biomolecular fractions from single samples (DNA, RNA, proteins, metabolites) Flexible design - Broad range of different sample types Cryo-preservation and bio-banking of samples & fractions Q1 2023
- 16. SINGLE CELL UNIT Units of the Raman Assisted Microfluidic Cell Sorting Using Optical Tweezers Microscale cultivation unit Single cell genomics Q2 2023 Microfluidics for cell sorting & characterization based on taxonomic & functional attributes, culture handling and processing for single cell genomics
- 17. MICROSCALE CULTIVATION UNIT Advanced systems for culturing of anaerobes at microcolony and single cell level Solid-phase porous aluminium oxide culture chip systems Suspended bead-based / emulsion systems Microbioreactor equipment for initial screening of natural & synthetic mixed communities Q1 2023
- 18. Shetty et al. (2022) NPJ Biofilms EXAMPLE FROM OUR OWN MICROBIOME Understanding gut functional microbial networks through synthetic microbiomes
- 19. GROWTH OF CONSORTIUM MEMBERS Shetty et al. (2022) NPJ Biofilms Monocultures 10-species mixed culture
- 20. EXPAND TO PARALLEL REACTOR DESIGN Shetty et al. (2022) ISME J
- 21. - acetate + B.hyd REPRODUCIBLE BEHAVIOR OF CONSORTIUM Shetty et al. (2022) ISME J
- 22. BIODISCOVERY PLATFORM Isolation and high-throughput cultivation of micro- organisms and consortia Single cell platform Geared towards strict anaerobes Automated sample processing platform Looking forward to welcome you at the Biodiscovery and other Platforms at UNLOCK
- 24. UNLOCK at TU Delft: An engineering approach to microbial ecology PARALLEL CULTIVATION PLATFORM
- 25. QUANTITATIVE MICROBIAL PHYSIOLOGY @ TU DELFT Sef Heijnen Gijs Kuenen Mark van Loosdrecht
- 26. UNLOCK-DELFT – Parallel Cultivation Facility: 40 bioreactors BIOREACTOR SET-UP Created with BioRender
- 28. FOR WHOM? Any research question that can be translated to a laboratory bioreactor experiment!
- 29. WHAT'S NEW? Parallel experiments Comparative system analysis
- 30. WHAT'S NEW? Parallel experiments Comparative system analysis On-line measurements Off-gas Mass Spectometry
- 31. WHAT'S NEW? Parallel experiments Comparative system analysis On-line measurements Off-gas Mass Spectometry Dynamic operation System identification
- 33. Sequential and/or parallel configuration of bioreactors Specifically suitable for sustainable solutions for environmental challenges MODULAR BIOREACTOR PLATFORM
- 34. TYPE OF REACTORS Standard bioreactors Bio-electrochemical systems High P/T reactors Constructed Wetlands
- 35. Created with BioRender TYPE OF REACTORS
- 36. MIX AND MATCH Mix and Match (some examples) Reactors in sequence (technology trains) for optimal removal, recovery, etc., for example Bioreactor and wetland as polishing step (or vice versa) Sandfilter and BES BES and bioreactors Etc.
- 37. MIX AND MATCH Mix and Match (some examples) Reactors in sequence (technology trains) for optimal removal, recovery, etc. Parallel configuration of various reactor types
- 38. MODULAR BIOREACTOR PLATFORM Mix and Match (some examples) Reactors in sequence (technology trains) Parallel configuration of various reactor types Biological Activated Carbon Sand Filter Moving Bed BioReactor
- 39. MODULAR BIOREACTOR PLATFORM Mix and Match (some examples) Reactors in sequence Parallel configuration Biological Activated Carbon Sand Filter Moving Bed BioReactor Week 1 Week 12 Week 1 Week 12 Week 1 Week 12 Hydrochlorothiazide Propaponolol Metoprolol Caffeine Trimethoprim Sulfamethoxazole Clarithromicin Naproxen Benzotriazole 4& 5methyl benzotriazole Chloridazon Carbamazepine Diclofenac Furosemide BAM Desphenyl chloridazon Mecoprop 2.4D MBBR BAC SF NA 0 20 40 60 80 >99 MP removal (%)
- 40. MODULAR BIOREACTOR PLATFORM Mix and Match (some examples) Reactors in sequence Parallel configuration of various reactor types Biological Activated Carbon Sand Filter Moving Bed BioReactor Constructed Wetlands
- 41. ANALYTICAL EQUIPMENT On line gas analyses Sensors Gas sample multiplexer 4 channels Mass Spectrometry On line liquid analyses Sensors NMR, coupled to autosampler and liquid handler LC-MS online (Q3 2024)
- 43. OVERVIEW
- 44. MODULAR BIOREACTOR PLATFORM Various reactor types in sequence (technology trains) for optimal removal, recovery, etc. Parallel configuration of various reactor types Coupling to inline and online measurements Looking forward to welcome you at the Modular and other Platforms at UNLOCK
- 46. Data storage, extraction and analysis of high- throughput data Findable, Accessible, Interoperable, Reusable by design FAIR DATA PLATFORM
- 47. Knowledge Pyramid PHILOSOPHY Information: Who, What, When = Organized Facts FAIRified RAW Data: Unorganized set of Facts RAW Data: Base Building Blocks Wisdom: Actionable Knowledge Knowledge: How to link Organized Facts and turn it into Knowledge
- 48. DATA COLLECTION & FAIRification FAIR by Design instead of data FAIRification after the experiment Project planning • Experimental design • Metadata template Experiments • Process registration • Metadata update Validate metadata • Inconsistency checks FAIR metadata • Data repository • Metadata included
- 49. FAIR DATA STATION Form generation Registration Validation Resource Application of the FAIR by Design principle makes high-level machine-actionable metadata available already at the start of the experiment This high-level metadata is used to manage the downstream processing of raw data
- 50. METADATA REGISTRATION – USER-FRIENDLY EXCEL WORKBOOK User ISA-tab
- 51. HIGH-LEVEL MACHINE-ACTIONABLE METADATA PROGRAMS - THE iRODS DMS FAIR-DS
- 52. FAIR DATA PLATFORM DATA USER INTERFACE Machine-Actionable Metadata programs the iRODS DMS to: Build and present to the user a hierarchical folder structure following the ISA metadata framework. Machine-Actionable Assay Metadata programs the iRODS DMS to: Automatically analyze high-throughput omics data and store results in the correct folders. Un-FAIR data cannot be properly stored and (automatically) processed! Synthetic & control data
- 53. HIGH-THROUGHPUT DATA ANALYSIS Standard state of the art “Omics” workflows are available off the shelf. Workflows are FAIR by design https://workflowhub.eu. Workflows produce provenance data] Workflow runs in Dockers
- 54. FEATURES (1) Central part of the UNLOCK Infrastructure. FAIR by design Experimental Design doubles as a Machine-Actionable Data Management Plan. Metadata driven data analysis workflows This leads to better experimental designs, a reduced data analysis workload, less mistakes and no loss of data.
- 55. FEATURES (2) The FAIR-data platform outputs are: Raw and transformed data, semantically linked to the experimental design, experiment metadata and workflow provenance. Your data, metadata, transformed data and provenance directly available on your desktop. For publication purposes: European Nucleotide Archive (ENA-)compatible metadata for submission of your sequence data. All output can be distributed as a digital object for publication purposes and further downstream analysis.
- 56. UNLOCK IN A NUTSHELL Sequential and/or parallel configuration of bioreactors Specifically suitable for sustainable solutions for environmental challenges Flexible arrangement of analytical equipment Cultivation of most chemo- and phototrophic microbial communities in extremely well-defined conditions Data storage, extraction and analysis of high- throughput data in a cloud-based infrastructure Findable, Accessible, Interoperable, Reusable by design Isolation and high-throughput cultivation of micro-organisms and consortia Geared towards strictly anaerobic micro- organisms Illustration by Haans Design
- 57. THE UNLOCK TIMELINE 2030 2023 2022 2021 2020 2018 Formal Start: September 1st, 2020 Opening: November 3rd, 2022 2025
- 58. SIMPLE PROCEDURE FOR TRANSNATIONAL ACCESS Excellence Open Science Created with BioRender
- 59. UNLOCK – DIFFERENT SERVICE LEVELS 3 access levels • Basic / Basic plus / All inclusive All Inclusiv e Basic Plus Wet/Dry Basic Plus Wet/Dry Basic Basic
- 60. UNLOCK – DIFFERENT SERVICE LEVELS All Inclusiv e Basic Plus Wet/Dry Basic Plus Wet/Dry Basic Basic Basic Service • Interactive project design • Bioreactor operations • Media • Online analyses • Data acquisition & storage • Microbiome storage • Training • Handling, operation & downstream analyses / interpretation by guest Subsidized for excellent, open science projects
- 61. UNLOCK – DIFFERENT SERVICE LEVELS All Inclusiv e Basic Plus Wet/Dry Basic Plus Wet/Dry Basic Basic Basic Plus Service • Reactor operation • Periodic sampling for offline & omics analyses • Offline chemical analyses • Tailor-made Omics analyses • Initial data processing & storage
- 62. UNLOCK – DIFFERENT SERVICE LEVELS All Inclusiv e Basic Plus Wet/Dry Basic Plus Wet/Dry Basic Basic All Inclusive Service • Full experimental setup definition and execution • Data processing, analysis and interpretation • Full technical report
- 63. MEET UNLOCK ONLINE - UNLOCKtober
Editor's Notes
- Microorganisms are everywhere. Evolution of the past 3.5 billion years has resulted in a microbial diversity that is so incredible and endless that it has been often compared to the number of stars in the universe. But why would you care? Why would we care? Because microorganisms shape who we are. We cannot live without the microbial communities that colonize our body. In fact, we are more microbe than human in terms of numbers of cells and genes. This is just one of the many examples where such complex microbial communities play essential roles in our daily lives. But this beautiful complexity ALSO is the reason why we still know so little about how these communities work, what they do in nature and what they can do for us.
- This is also the most important reason why Industrial biotechnology as we know it to date almost exclusively relies on isolated single microorganisms. All these single microorganisms that we managed to domesticate in our laboratories comprise much less than 1% of natural microbial diversity. So really they are just a tiny tip of the microbial universe that still holds so many secrets and promises. Of course, these single strain applications also do not take into account any of the interactions normally present in microbial communities.
- But it’s exactly these interactions that determine the function of such diverse microbial communities where different microbes like the ones you see here all form essential pieces of the puzzle in collaborative interdependent networks. Our lack of understanding is therefore also the reason why so many microorganisms remain uncultured. There has been consensus in the field that we need to dramatically step up our knowledge to unlock the full power of microbial communities as a whole for applications in e.g. global health and circular economy. Nature has already been circular for billions of years with a huge potential – so what have we been waiting for? What did we miss?
- Especially in Delft and Wageningen, our Environmental Biotechnology groups are very experienced in growing microbial communities in different types of bioreactors for different applications. Also, In Wageningen we are very good at isolating novel microbes from many different environments, and we have been among the pioneers in the use of a broad range of biomolecular, genomics-based methods to study the composition and function of communities. Last but certainly not least, we are at the forefront of handling and using data from such analyses according to FAIR principles. So WHAT is it that we are we missing? With all the necessary ingredients in place, the most important practical limitation has been the FRAGMENTATION OF EFFORTS – the fragmentation of the different fields of expertise. Just think about it - The almost endless diversity of microorganisms, and the shear complexity of their interactions are simply too much to handle for individual teams.
- Together, we felt that it was time for disruptive solutions! This is where the idea of the UNLOCK infrastructure was born. For the first time UNLOCK will provide the neccessary INTEGRATION, PARALLELISATION and STANDARDISATION of expertise, facilities and procedures that are so urgently needed to overcome current limitations
- UNLOCK for the first time provides a true One Stop Shop comprising 4 complementary and fully integrated platforms that we will describe in more detail a bit later today. Two bioreactor platforms located in Delft and Wageningen provide the necessary hardware to grow and study microbial communities under a broad range of different conditions. The highly automated biodiscovery platform then provides specialty equipment that allows for highly standardized processing and biomolecular analysis of samples from these systems. It also allows for the discovery and characterization of yet uncultivated microorganisms and their mixtures at the single cell level – essential for the design of synthetic microbial consortia beyond the state of the art! The unique strength of UNLOCK then really lies in the tight integration of these three experimental platforms with the FAIR data platform
- UNLOCK builds on a long tradition of Dutch microbiologists. Among these, Antonie van Leeuwenhoek, the first person to actually see a microorganism with his own eyes using his microscope, and Martinus Beijerinck are just two of many examples. Call it co-incidence or fate – Martinus Beijerinck in fact worked both in Wageningen as well as in Delft.
- This tradition continues to date, best exemplified by the fact that five contemporary Dutch microbiologists, including 2 each from our Wageningen and Delft teams, have recently obtained the Spinoza price – best known as the Dutch Noble Price!
- Building on the long history of unique and productive collaborations between our Delft and Wageningen teams with shared interests and complementary expertise, UNLOCK is the logical next step, leading the way into a new era of microbial community research. UNLOCK can also tap into our global network of collaborators – of course all potential users.
- Enough introduction for now. The main reason for all of you joining us here today is of course that we want to officially unlock UNLOCK, an open infrastructure for exploring new horizons for microbiome research
- Let’s now take a dive into the heart of UNLOCK – its 4 platforms
- At our first pitstop, we will visit the BIODISCOVERY PLATFORM
- The BIODISCOVERY PLATFORM is located in Wageningen, and actually right here in Impulse. You will have the opportunity to visit the BIODISCOVERY LAB later this afternoon. The highly automated biodiscovery platform provides specialty equipment that allows for highly standardized processing and biomolecular analysis of samples from for example bioreactor systems operated at the other platforms, or any other sample type you might be working with. It also allows for the discovery and characterization of yet uncultivated microorganisms and their mixtures at the single cell level – essential for the design of synthetic microbial consortia beyond the state of the art! To this end, focus of our installations will be particularly geared towards anaerobic micro-organisms.
- The BIODISCOVERY PLATFORM has three main installations The Sample Processing Unit A microfluidic cell sorting unit And single cell- and microscale cultivation platforms
- So again – to summarize – the BIODISCOVERY PLATFORM provides for the necessary equipment to characterize, isolate and culture microorganisms at the single cell to millilitre scale, and is geared towards anaerobic microbes.
- The next stop – the PARALLEL CULTIVATION PLATFORM
- Biological experiments using different instruments will create operational datastreams and in most cases discrete omics type datasets. Like a spider in this web of data, the FAIR data platform collectsll this data and transforms it in information
- On the left we see the knowledge pyramid and as we climb up the ladder to obtain Actionable knowledge there are a number of hurdles to be taken including data storage and fairification. Users are responsible for their own data however n the unlock proposal we promised that all data produced in Unlock would Findable Accessible and Interoperable. That is why, out of the box we provide proper long-term storage. In addition we will help with proper data fairification, data organization and standard data crunching of for instance omics data in an effort to reach the Information level. Next to this standard package as part of the operational procedure of the Unlock Infrastructure we can of course assist in turning Information into knowledge by pointing at visualization and modelling tools and are willing further collaborate on that on a case by case basis.
- A key property of FAIR DATA PLATFORM that we have adopted the FAIR by Design principle which entails thinking about the metadata already at the planning phase. Normally data fairification takes place after the data is analysed as we see in for instance the GOFAIR data pfariifcation pipeline the but as the metadata plays an important role already the data analysis we think it is better to collect the right kind of metadata already the planning phase. Another advantage is that when this is done properly that the addition of high level metadata can turn your experimental design into machine-actionable data management and data processing plan. I will show you how in a minute
- To capture and validate machine actionable metadata we have developed the FAIR DATA Station. It is part of the unlock data infrastructure but can also be run as a freely available standalone tool. The tool follows a simple three step procedure based on the generic investigation study assay metadata model the users select the appropriate minimal metadata model as a template to generate a pre-formatted Excel Workbook. Per sample the user fills in the mandatory metadate one row per sample upon which a validation procedure included for checking for the expected format for registered values.
- Here we see an example Excel Workbook following the ISA model. Excel was chosen because most Users know how to use it, Excel can be used off-line and on many devices and out of the box supports collaborative efforts. Column headers align with the chosen minimal information model (s) and are semantically interoperable.
- This is the Unlock compute infrastructure. It is built around around an iRODS data management system hosted at SURF. As we see on right Investigation and Study metadata extracted from the excel workbook prepares iRODS to receive your experimental data. Using the metadata this, iRODS will then automatically take care of the data backup and findability and accessibility of the data using the metada registered at the Investigation and Study level. Assay metadata is used to automatically handle omics data using standard pipeline written in the common workflow language.
- On the left we see the iRODS user interface. It acts like a read-only network drive and is highly structured. This is data obtained form an experiment done at the MODULAR BIOREACTOR PLATFORM. The hierarchical folder structure follows the Investigation Study Assay metadata framework. In this study a number of different fermenter types were used, in extended ISA model they are called observation units from which samples were taken for Amplicon analysis using a tool called NGTAX. Under Assay we see the quality control, classification data provenance , raw data etc logically linked to the sample taken. The folder structure is driven by the metadata provided by the user. We see the excel file on top and the conversion of that in RDF. At the bottom of the list we see the synthetic and control data used to monitor the data transformation process. Note that with this system Un-FAIR data cannot be properly stored and processed. High-level Machine-Actionable Metadata programs the iRODS DMS to: Build and present to the researcher a hierarchical folder structure following the ISA metadata framework. And to Automatically store and backup Raw Data semantically linked to the available metadata. Machine-Actionable Assay Metadata subsequently programs the iRODS DMS to: Automatically analyze high-throughput omics data and store results in the correct folder. -- Un-FAIR data cannot be processed!
- Next to a amplicon analysis workflow We have developed more than 10 other state of art omics analysis workflows that produce there own provenance data. All workflows are containerized, use version control and have been tested using synthetic data and are FAIR by design. All are freely available at the workflow hub. Since in Unlock the the user metadata controls the workflows, the analysis requires minimal human interaction and results will be automatically available in the predefined folders.
- So again – UNLOCK will provide a unique ONE-STOP-SHOP comprising 4 complementary and fully integrated platforms platforms. The unique strength of UNLOCK then lies in the tight integration of the three experimental platforms with the FAIR data platform
- Let me tell you a bit more about the timelines for UNLOCK.
- To streamline the foreseen strong interest of potential users in working in the UNLOCK facilities, an easy and efficient access procedure is in place. Proposals submitted by users will be evaluated and selected several times per year based on excellence by independent reviewers, with the most important goal to allow those excellent, enthusiastic researchers to start working on their brilliant ideas as fast as possible. Hence, UNLOCK with all its features has been designed to enable truly excellent science. In addition, it will also possible to use UNLOCK facilities on a pay-per-use basis. I should mention that this will be limited to a maximum of 10-20 % of our capacity due to state aid regulations.